The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Bile Flow Dynamics in Patients with Cholelithiasis: An Evaluation with Cine-Dynamic Magnetic Resonance Cholangiopancreatography Using a Spatially Selective Inversion-Recovery Pulse

Background: A variety of pathophysiological changes in the biliary system occur in patients with cholelithiasis, but the changes in the bile flow dynamics in those patients remain unclear. The purpose of this study was to elucidate the changes in the bile flow dynamics in patients with cholelithiasis using cine-dynamic magnetic resonance cholangiopancreatography (MRCP) with a spatially selective inversion-recovery (IR) pulse. Methods: We retrospectively examined 25 patients with gallstones (gallstone group) and 69 patients without gallstones (non-gallstone group) who underwent abdominal MRI, including in- and opposed-phase T1-weighted images and cine-dynamic MRCP with a spatially selective IR pulse. The frequency and secretion grade of the antegrade and reverse flow of the bile on the cine dynamic MRCP images and the signal intensity ratio (SIR) of the gallbladder in the in- and opposed-phase T1-weighted images were evaluated. Results: The frequency and mean secretion grade of the antegrade bile flow were significantly higher in the gallstone group than in the non-gallstone group (p = 0.011 and p = 0.003), while no significant differences in those values of the reverse bile flow were found between the two groups. The SIR of the gallbladder in the T1-weighted gradient-echo in-phase images was significantly lower in the gallstone group than in the non-gallstone group (p = 0.004). Conclusions: Cine-dynamic MRCP with a spatially selective IR pulse can noninvasively visualize changes in the bile flow dynamics of patients with gallstones

Healthcare Application of In-Shoe Motion Sensor for Older Adults: Frailty Assessment Using Foot Motion during Gait

Frailty poses a threat to the daily lives of healthy older adults, highlighting the urgent need for technologies that can monitor and prevent its progression. Our objective is to demonstrate a method for providing long-term daily frailty monitoring using an in-shoe motion sensor (IMS). We undertook two steps to achieve this goal. Firstly, we used our previously established SPM-LOSO-LASSO (SPM: statistical parametric mapping; LOSO: leave-one-subject-out; LASSO: least absolute shrinkage and selection operator) algorithm to construct a lightweight and interpretable hand grip strength (HGS) estimation model for an IMS. This algorithm automatically identified novel and significant gait predictors from foot motion data and selected optimal features to construct the model. We also tested the robustness and effectiveness of the model by recruiting other groups of subjects. Secondly, we designed an analog frailty risk score that combined the performance of the HGS and gait speed with the aid of the distribution of HGS and gait speed of the older Asian population. We then compared the effectiveness of our designed score with the clinical expert-rated score. We discovered new gait predictors for HGS estimation via IMSs and successfully constructed a model with an “excellent” intraclass correlation coefficient and high precision. Moreover, we tested the model on separately recruited subjects, which confirmed the robustness of our model for other older individuals. The designed frailty risk score also had a large effect size correlation with clinical expert-rated scores. In conclusion, IMS technology shows promise for long-term daily frailty monitoring, which can help prevent or manage frailty for older adults

Pancreatic Steatosis Evaluated by Automated Volumetric CT Fat Fraction of the Pancreas: Association with Severity in COVID-19 Pneumonia

This study investigated the relationship between the severity of pneumonia based on chest CT findings and that of pancreatic steatosis assessed using an automated volumetric measurement of the CT fat volume fraction (CT-FVF) of the pancreas, using unenhanced three-dimensional CT in polymerase chain reaction (PCR)-confirmed COVID-19 patients. The study population consisted of 128 patients with PCR-confirmed COVID-19 infection who underwent CT examinations. The CT-FVF of the pancreas was calculated using a histogram analysis for the isolation of fat-containing voxels in the pancreas. The CT-FVF (%) of the pancreas had a significantly positive correlation with the lung severity score on CT (ρ = 0.549, p p < 0.01). The area under the curve of CT-FVF (%) of the pancreas in predicting the severity of pneumonia on CT was calculated to be 0.82, with a sensitivity of 88% and a specificity of 68% at a threshold for the severity score of 12.3. The automated volumetric measurement of the CT-FVF of the pancreas using unenhanced CT can help estimate disease severity in patients with COVID-19 pneumonia based on chest CT findings